Nog is asked about his job with security. Jake whispers something and it is revealed that Nog has problems with the Klingons who ignore him because he is a Ferengi.

Then GeneralMartok enters the room and explains to Sisko that his ship has intercepted an encrypted message from the Maquis. This is a surprise to both men, who believed the Maquis were completely wiped out by the Dominion. The message states that missiles have been launched heading for Cardassia. Although Martok couldn't find any missiles, he explains that the Klingon Empire had provided the Maquis with cloaking devices to aid them against Cardassia. Sisko knows that if Cardassian citizens are killed by Human terrorists, the Dominion will launch a counter strike that will surely start a war.

Captain Sisko visits ex-commander Michael Eddington in prison. Eddington denies that the message about the missiles involves him. He says he has nothing to do with the Maquis anymore, that they are all dead, and they cannot be reborn. Eddington insists that the missiles are completely undetectable, and that nothing can be done to stop them. Sisko offers Eddington a path to eventual freedom if he will help find and destroy the missiles, but Eddington insists that he will be perfectly happy to wait in his cell until the missiles hit their target and the Dominion destroys his prison in their inevitable counterstrike.

Quark is in the infirmary treated by Dr. Julian Bashir. It appears that Morn attacked Quark with a barstool. Quark claims it was unprovoked but Kira Nerys and Odo reveal that Quark told Morn that Deep Space 9 is the first target if the Dominion attack – and if that happens, there is no chance of survival. Thus, Morn responded with panic by running down the Promenade screaming "We're all doomed!" Later, Sisko contacts Kira on DS9 explaining that he is going to the Badlands. Kira wants to send the Defiant, but Sisko tells her he is not alone, and he reveals Eddington on board the runabout.

Eddington philosophizes about food and Maquis morals. He suggests that Sisko's fight against the Maquis is personally driven. Eddington says that Sisko's former old friend Cal Hudson was killed in a skirmish with the Cardassians. Sisko feels regret, and Eddington presses the point by saying that Cal thought Sisko was wrong about the Maquis, but he didn't hold that against Sisko.

Eddington taunts Sisko by saying Sisko doesn't blame the Maquis for their philosophy but he blames the Starfleet officers who betrayed their Oaths by joining the Maquis in the first place, telling Sisko that the Maquis were no threat to Starfleet--only a threat to Sisko's record. Sisko is quickly able to counter by saying that Eddington's leadership of the Maquis was so effective against the Cardassians that it forced them to ally with the Dominion, setting the stage for a war between the Federation and the Dominion that could lead to the deaths of millions. Eddington is clearly affected by this, and sits down with his back to Sisko in a contemplative mood.

Back on DS9, Nog and Jake are sitting in Quark's. Nog waits for the Klingons to get louder so he can send them to the brig for disturbance. When they exceed 70dB, Nog laughs and prepares to arrest them, but he falls from his chair and the Klingons laugh at him.

Sisko and Eddington are attacked by the Jem'Hadar. Sisko tests Eddington's death wish, calling his bluff. He takes off his handcuffs and leaves him to steer the ship. Eddington is able to shake the Jem'Hadar off, but they soon return. Using the Maquis trick of igniting the nebula gases they destroy the Jem'Hadar and head for the missile base.

For Nog, the last straw is seeing Martok and two of his aides lingering on the Promenade, in his and Jake's "favorite spot." To Jake's incredulity, Nog marches up to the Klingons and orders them to move on, or else he will be forced to arrest them for loitering, strictly prohibited by station rules. Martok bellows that the young Ferengi is either courageous or a fool to threaten him with arrest. Nog trembles, but stands his ground. Martok begins to laugh, acknowledging the young Ferengi's gumption, and he instructs his aides to move on.

Meanwhile the runabout arrives at the missile base. They are suddenly attacked by the Jem'Hadar. Sisko fights them hand to hand while Eddington shoots them from cover.

They discover that all the Maquis followers are dead. Eddington is filled with guilt and remorse, feeling that he should have done more to help his followers and friends. Sisko sadly notes that perhaps it was the Federation who truly failed the Maquis, and maybe something could have been done to prevent this tragedy. Regardless, Sisko insists on disarming the missiles, but then they find a small group of hidden survivors. One of them is Eddington's wife. It is revealed that no missiles actually exist, that the encoded message just said that the Maquis arrived safely at the meeting point. It was all a ruse to get Eddington out of jail and to trick Sisko into bringing him to the chosen destination.

More Jem'Hadar troops arrive. Eddington tells Sisko to save the people, and he stays behind to fight off the oncoming troops. He is killed in the attacks, but his sacrifice gives Sisko and the Maquis followers time enough to safely escape. The runabout leaves the Badlands, and Rebecca sits distraught at the loss of her husband.

Back on the station, Nog brings Major Kira her lost earring loop, which he found after an exhaustive search of the areas she was working on the day before. The young Ferengi's industriousness and ingenuity continue to astound his superiors; Kira congratulates him on it, and he replies, "just doing my job." Entering a turbolift, they run into Martok stepping off. Looking up from his PADD, he greets Nog, "Cadet," and Nog replies with an equally brief "General." Nog beams as he and Kira step onto the turbolift.

Dax and Sisko talk about Eddington and the Maquis. Sisko admits that Eddington is not a traitor but was loyal to what he believed in until the very end. Dax asks if that's what it is, the end of the Maquis. Sisko is unsure about that, as there may be others out there who escaped the Dominion, biding their time and waiting for their chance to strike. And besides, Sisko muses, there's always something romantic about a lost cause. Dax tells Sisko that he almost sounds hopeful and leaves. Sisko then stares out of the window, thinking about Eddington.

"Witnesses say you were talking to him [Morn] right up to the second he went berserk."
"Of course I was talking to him. That's what bartenders are supposed to do. Talk to their customers."
"And what exactly was it that you were talking to him about?"
"All I said was that the military personnel on this station were starting to look a little nervous. And when they get nervous, I get nervous."
"That's all you said?"
"Basically... I might've done a little harmless theorizing."
"About what?"
"Oh... something like... it was only a matter of time before the Dominion launched a full-scale assault on the Federation and that when that happened the station would undoubtedly be their first target... and I might've idly suggested that there wasn't a hope in hell of any of us getting out of here alive."
"And that's when he hit you with the barstool and ran out onto the Promenade screaming 'We're all doomed'."
"Some people just don't react well to stress."

"You are either very brave, or very stupid, Ferengi!"
"Probably a little of both."
(Laughing) "Indeed. Courage comes in all sizes. (Pointing to his missing eye) But don't tempt fate."

- Martok and Nog

"This wasn't supposed to happen. We were winning. The Cardassian Empire was falling into chaos. The Maquis colonies were going to declare themselves an independent nation."

- Eddington

"I can barely see two meters in front of me. How will I know what I'm aiming at?"
"I'll be the one holding the pipe."
"Attacking two Jem'Hadar soldiers with a pipe? That's a brilliant plan."
"It could be worse."
"I know. It could be me holding the pipe."
"Exactly."

- Michael Eddington and Benjamin Sisko

"You have sharp eyes."
"Not really. I just waited to see which of you was knocked down first and then I shot the one still standing."
"Thank you for your vote of confidence."

Ira Steven Behr decided to end the Michael Eddington/Maquis story arc because he felt that there were too many open threads leading into the sixth season, and he wanted to get some closure on at least one of them. Behr explains, "We were just desperate to finish something off. We had to finish a thread. It was necessary. We just had so many things. So I told them, 'We are going to end something and then not hear about it again'!" Indeed, Behr wanted to officially kill off every single member of the Maquis, but Rick Berman wouldn't allow him to do this in case Voyager wanted to use them at some stage in the future. As far as the Deep Space Nine writers were concerned however, the Maquis story arc was over. (Star Trek: Deep Space Nine Companion)

The holding cell where Sisko visits Eddington is a re-dress of the USS Voyagerbrig set, moving the cell from a point to frame right of the door to directly across from it. This version of the set would be seen again in the episode "Waltz", this time with a stretch of USS Defiant corridor erected outside to serve as the interior of the USS Honshu, and again in "The Magnificent Ferengi" as the brig of an unnamed Regula-type starbase.

After this episode aired, and the Eddington story arc officially ended, many fans found the character of Eddington a little difficult to pin down, some loved him, some hated him, many others were a little unsure of him. This sense of uncertainty is shared by Ira Steven Behr himself, "I still haven't figured him out. Do we like him? Do you not like him? Was he good? Bad? A pain in the ass? I'm not sure." Even Sisko appears to have trouble reaching a conclusion as regards the essence of Eddington's character. The final scene in the episode, between himself and Dax as he tried to come to terms with who Eddington was and what he stood for, was written precisely to try to get to the core of Eddington's raison d'être, not just for Sisko, but for the audience and the writers as well. According to Behr, "I felt it was very important to try to make sense of the man Eddington was. We owed it to Sisko to give him some kind of closure, some kind of understanding. On top of everything else, he let the guy die, basically." (Star Trek: Deep Space Nine Companion)

News of the destruction of the Maquis at the hands of the Dominion was later sent to former Maquis member Chakotay in VOY: "Hunters", when Starfleet used a Hirogen communications network to transmit personal letters to the crew of the USS Voyager in the Delta Quadrant.